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- PDB-3zj4: Neurospora Crassa Catalase-3 expressed in E. coli, triclinic form. -

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Basic information

Entry
Database: PDB / ID: 3zj4
TitleNeurospora Crassa Catalase-3 expressed in E. coli, triclinic form.
ComponentsCATALASE-3
KeywordsOXIDOREDUCTASE / HYDROGEN PEROXIDE / PEROXIDASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase / Catalase immune-responsive domain ...Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase-3
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.098 Å
AuthorsZarate-Romero, A. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3
Authors: Zarate-Romero, A. / Stojanoff, V. / Rojas-Trejo, S.P. / Hansberg, W. / Rudino-Pinera, E.
History
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE-3
B: CATALASE-3
C: CATALASE-3
D: CATALASE-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,6758
Polymers330,2094
Non-polymers2,4664
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54520 Å2
ΔGint-279.8 kcal/mol
Surface area72670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.445, 88.207, 104.398
Angle α, β, γ (deg.)82.08, 82.48, 62.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CATALASE-3


Mass: 82552.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: BEFORE RESIDUE 1 A HIS TAG SIGNATURE IS PRESENT / Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C169, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE
Crystal growpH: 7.5 / Details: 100MM HEPES PH 7.5, 20 PERCENT PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2010
Details: SI(111) CHANNEL CUT MONOCHROMATOR, TOROIDAL FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→29.5 Å / Num. obs: 47857 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.66 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.5
Reflection shellResolution: 3.1→3.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJ6

3ej6


Resolution: 3.098→29.399 Å / SU ML: 0.36 / σ(F): 1.96 / Phase error: 24.05 / Stereochemistry target values: ML
Details: RESIDUES 37 TO 716 ARE VISIBLE IN THE ELECTRON DENSITY MAP. NCS WERE USED UNTIL THE LAST STEP OF THE REFINEMENT IN WHICH AFTER A NORMALISATION OF THE COORDINATES A RIGID BODY REFINEMENT WERE USED.
RfactorNum. reflection% reflection
Rfree0.2455 2424 5.1 %
Rwork0.1969 --
obs0.1994 47852 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.8 Å2
Refinement stepCycle: LAST / Resolution: 3.098→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21333 0 172 0 21505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322065
X-RAY DIFFRACTIONf_angle_d0.86429988
X-RAY DIFFRACTIONf_dihedral_angle_d18.0287920
X-RAY DIFFRACTIONf_chiral_restr0.0593161
X-RAY DIFFRACTIONf_plane_restr0.0053978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0978-3.16090.3441350.29192619X-RAY DIFFRACTION96
3.1609-3.22960.29231610.25972599X-RAY DIFFRACTION99
3.2296-3.30460.31671380.25542687X-RAY DIFFRACTION99
3.3046-3.38720.25961320.24162675X-RAY DIFFRACTION99
3.3872-3.47860.31351510.23762678X-RAY DIFFRACTION99
3.4786-3.58080.24691370.2232668X-RAY DIFFRACTION99
3.5808-3.69620.25771380.22172681X-RAY DIFFRACTION99
3.6962-3.8280.29481440.20952697X-RAY DIFFRACTION99
3.828-3.98090.24841390.1982654X-RAY DIFFRACTION99
3.9809-4.16160.22431280.18322682X-RAY DIFFRACTION99
4.1616-4.38030.22371570.16912668X-RAY DIFFRACTION99
4.3803-4.65380.21531360.172693X-RAY DIFFRACTION99
4.6538-5.01150.21991400.15812689X-RAY DIFFRACTION99
5.0115-5.51280.21031670.16212669X-RAY DIFFRACTION99
5.5128-6.30370.20671330.16922697X-RAY DIFFRACTION99
6.3037-7.91620.20811480.17212674X-RAY DIFFRACTION99
7.9162-29.39990.21031400.15482698X-RAY DIFFRACTION99

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